AMBER Archive (2006)

Subject: Re: AMBER: one question about mm_pbsa

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Thu Apr 06 2006 - 16:48:20 CDT

Hi, Yongchun

MM-PBSA don't use the explicit solvent. The solvation effect is simulated
with the continuum solvation model. You may need to remove your explicit
solvent and counter ions when performing MM-PBSA calculations!

If you've already removed explicit solvents and just want the MM energy be
calculated with periodic boundary conditions, I think this doesn't make
sense and is incorrect.

Regards!

Liu

On Wed, 05 Apr 2006 03:47:06 -0300, 杜永春 <duyongchun_at_mail.nankai.edu.cn>
wrote:

> hi,Amber
> I use mm_pbsa programe to compute binding energy.There is a periodic
> boundary
> in my prmtop file .But when running ,it creates a sander_com.in file.In
> this file
> ,the NTB=0,whith means that no periodicity is applied.How can I modify
> the
> mm_pbsa.in file and then I can change the NTB?Thanks!
> Yongchun Du
> 2006.4.5
>
>
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-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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